High abundance of lactobacilli in the gut microbiome of honey bees during winter
Data files
Mar 25, 2025 version files 6.28 MB
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16s_MAPs_GB_H_(1).txt
7.39 KB
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16Staxabarplots_clean2_(4).qzv
998.59 KB
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alpha_amp.csv
14.32 KB
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Alpha_diversiy_R_file.docx
119.38 KB
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alpha_rarefaction_(2).qzv
745.60 KB
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jaccard_emperor.qzv
978.44 KB
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README.md
2.52 KB
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Species_level_abundance.csv
216.64 KB
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stats-dada2_(3).qzv
1.23 MB
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unweighted_unifrac_emperor.qzv
981.20 KB
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weighted_unifrac_emperor.qzv
981.15 KB
Abstract
Honey bee gut microbiota play specific roles in promoting host growth and physiology by regulating the immune system, behavior, metabolism, and neurological processes. While the gut microbiota of honey bee queens, workers, and larvae has been extensively studied, less is known about the composition of gut microbiota in the winter worker bees. This study investigates the dynamics of the gut microbiota in overwintering adult worker bees, focusing on two commercial bee strains: Bolton™ bees and Mann Lake™ bees. These Apis mellifera strains were investigated under different storage conditions (indoor storage at 6°C and outdoor storage in natural conditions) during the winter months (October, November, and December). Utilizing 16S rRNA gene amplicon sequencing, we characterized the microbial composition of the whole gut. We observed the Lactobacilli dominated in all the overwintering honey bee guts with a significantly higher abundance of unclassified Lactobacillus species in November, while Lactobacillus apis showed significantly higher abundance in October. Bolton bees exhibited higher abundance levels of Bartonella, Bifidobacterium, and Wolbachia, while Mann Lake bees showed increased abundance of Commensalibacter. Our results suggest that alpha diversity is influenced by the month rather than by the bee strain or storage conditions. We also found significant differences in beta diversity by month. Overall, taxonomical abundance was not affected by whether the hives were stored outside or in constant temperature indoor storage. However, various bacterial species showed differences in abundance across different months, with slight variations observed between bee strains. Given the potential benefits of the honey bee gut microbiome for health and nutrition, our data suggests that the genus Lactobacillus may play a significant role in bee health during winter and overwintering storage.
https://doi.org/10.5061/dryad.rxwdbrvjf
All .qzv file must be downloaded and uploaded to https://view.qiime2.org/ (opens in new window)
alpha_rarefaction(2).qzv: represents alpha rarefaction- sequences
16Staxabarplots_clean2.qzv: Relative abundances of the bacteria presented in Honey bee adults
16s_MAPs_GB_H (1).txt: represents metabarcode sequences used for sequencing
stats-dada2.qzv: file represents filtered, denoised, merged and non chimeric reads
unweighted_unifrac_emperor.qzv: A QIIME 2 visualization file displaying beta-diversity analysis using the unweighted UniFrac metric, which measures phylogenetic distances between microbial communities based on the presence or absence of taxa, visualized as an Emperor plot for sample clustering.
jaccard_emperor.qzv: A QIIME 2 visualization file containing an Emperor plot that represents beta-diversity analysis using the Jaccard distance metric, which measures dissimilarity between microbial communities based on the presence or absence of taxa, and can be viewed using QIIME 2 View.
weighted_unifrac_emperor.qzv: A QIIME 2 visualization file displaying beta-diversity analysis using the weighted UniFrac metric, which measures phylogenetic distances between microbial communities by considering both the presence and abundance of taxa, visualized as an Emperor plot for sample clustering. This file can be viewed using QIIME 2 View.
Alpha_diversiy_R_file.docx: An R script performing Generalized Linear Mixed Models (GLMMs) to analyze alpha diversity metrics (e.g., Shannon index) in honey bee gut microbiomes across months and storage status.
alpha_amp.csv: A CSV file containing alpha diversity metrics (e.g., Observed OTUs, Shannon, Simpson, invSimpson, Chao1, ACE) for each honey bee gut microbiome sample, including metadata such as SampleID, barcode sequence, month, bee type, hive status, and replicate information. This data is used to assess microbial diversity within individual samples.
Species_level_abundance.csv: This file contains taxonomic abundance data for microbial species identified in the gut microbiome of honey bees (Apis mellifera). The data is organized by sample, bee type, month of collection, bee status (e.g., inside or outside the hive), microbial species, and their relative abundance (in percentages).